Biology subjects

Ortabozkoyun, H.

Publications and source records attributed to Ortabozkoyun, H..

3 recordsLinked to original sources

bioRxiv2026

PDS5A and TOP2B cooperate for chromatin recruitment via CTCF

PDS5A, a regulatory subunit of the cohesin complex, and topoisomerase IIB (TOP2B), an enzyme resolving DNA topological problems, interact with CTCF and regulate transcription, chromatin loops, and genome organization. Yet, how PDS5A and TOP2B are recruited to chromatin to exert their function is not well-understood. Here, we studied the functional relationship between PDS5A and TOP2B and the resultant impact on genome organization and gene expression. Interestingly, TOP2B-PDS5A cooperate for their recruitment to CTCF-bound chromatin sites. The presence of catalytically active TOP2B increased PDS5A occupancy genome-wide. Notably, a novel PDS5A-CTCF interaction region in the CTCF N-terminal 95-116aa was required for CTCF-PDS5A-TOP2B interaction in vitro as well as for active TOP2B-mediated enrichment of PDS5A chromatin occupancy in vivo. The loss of CTCF(95-116aa) led to a reduced number of chromatin loops and dysregulated gene expression. In gliomas, PDS5A and TOP2B expression levels are variable and correlated, contributing to apparent heterogeneity in gene expression. Indeed, inducible knockdown of PDS5A led to reduced TOP2B occupancy and altered gene expression in the glioma genome. Importantly, PDS5A mediated sensitivity to TOP2 cancer drugs in glioma cells. This newly recognized functional interaction between PDS5A and TOP2B at chromatin boundaries clarifies the mechanisms fostering gene regulation through genome organization, with implications for glioma therapeutics.

biochemistry↗

bioRxiv2023

Novel Chromatin Insulating Activities Uncovered upon Eliminating KnownInsulators in vivo

Partitioning of repressive from actively transcribed chromatin in mammalian cells fosters cell-type specific gene expression patterns. While this partitioning is reconstructed during differentiation, the chromatin occupancy of the key insulator, CTCF, is unchanged at the developmentally important Hox clusters. Thus, dynamic changes in chromatin boundaries must entail other activities. Given its requirement for chromatin loop formation, we examined cohesin-based chromatin occupancy without known insulators, CTCF and MAZ, and identified a family of zinc finger proteins (ZNFs), some of which exhibit tissue-specific expression. Two such ZNFs foster chromatin boundaries at the Hox clusters that are distinct from each other and from MAZ. PATZ1 was critical to the thoracolumbar boundary in differentiating motor neurons and mouse skeleton, while ZNF263 contributed to cervicothoracic boundaries. We propose that these insulating activities act with cohesin, alone or combinatorially, with or without CTCF, to implement precise positional identity and cell fate during development.

genetics↗

bioRxiv2018

LEDGF and HDGF2 relieve the nucleosome-induced barrier to transcription

FACT (facilitates chromatin transcription) is a protein complex that allows RNAPII to overcome the nucleosome-induced barrier to transcription. While abundant in undifferentiated cells and many cancers, FACT is not abundant or is absent in most tissues. Therefore, we screened for additional proteins that might replace FACT upon differentiation. Here we report the identification of two such proteins, LEDGF and HDGF2, each containing two HMGA-like AT-hooks and a PWWP methyl-lysine reading domain known to bind to H3K36me2 and H3K36me3. LEDGF and HDGF2 localize with H3K36me2/3 at genomic regions containing active genes, usually adjacent to H3K27me3 domains. In myoblasts, where FACT expression is low, LEDGF and HDGF2 are enriched on most active genes. Upon differentiation to myotubes, LEDGF levels decrease across the genome while HDGF2 levels are maintained. Moreover, HDGF2 is recruited to the majority of myotube up-regulated genes and is required for their proper expression. HDGF2 knockout myoblasts exhibit an accumulation of paused RNAPII proximal to the first nucleosome within the transcribed region of many HDGF2 target genes, indicating a defect in early elongation. We propose that LEDGF and HDGF2 substitute for FACT in differentiated tissues and that their distribution on the genome helps maintain transcriptional programs unique to particular cell types.\n\nOne Sentence SummaryChromatin bound LEDGF and HDGF2 proteins allow RNAPII to overcome the nucleosome-induced block to transcription.

molecular biology↗